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Walkowski WG, Richards-Zawacki CL, Gordon WC, Bazan NG, Farris HE. The relationship between spectral signals and retinal sensitivity in dendrobatid frogs. PLoS One 2024; 19:e0312578. [PMID: 39541311 PMCID: PMC11563434 DOI: 10.1371/journal.pone.0312578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024] Open
Abstract
Research on visually driven behavior in anurans has often focused on Dendrobatoidea, a clade with extensive variation in skin reflectance, which is perceived to range from cryptic to conspicuous coloration. Because these skin patterns are important in intraspecific and interspecific communication, we hypothesized that the visual spectral sensitivity of dendrobatids should vary with conspecific skin spectrum. We predicted that the physiological response of frog retinas would be tuned to portions of the visible light spectrum that match their body reflectance. Using wavelength-specific electroretinograms (ERGs; from 350-650 nm), spectrometer measurements, and color-calibrated photography of the skin, we compared retinal sensitivity and reflectance of two cryptic species (Allobates talamancae and Silverstoneia flotator), two intermediate species (Colostethus panamansis and Phyllobates lugubris), and two conspicuous aposematic species (Dendrobates tinctorius and Oophaga pumilio). Consistent with the matched filter hypothesis, the retinae of cryptic and intermediate species were sensitive across the spectrum, without evidence of spectral tuning to specific wavelengths, yielding low-threshold broadband sensitivity. In contrast, spectral tuning was found to be different between morphologically distinct populations of O. pumilio, where frogs exhibited retinal sensitivity better matching their morph's reflectance. This sensory specialization is particularly interesting given the rapid phenotypic divergence exhibited by this species and their behavioral preference for sympatric skin reflectances. Overall, this study suggests that retinal sensitivity is coevolving with reflective strategy and spectral reflectance in dendrobatids.
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Affiliation(s)
- Whitney G. Walkowski
- Neuroscience Center, School of Medicine, LSUHSC, New Orleans, LA, United States of America
- Department Cell Biology and Anatomy, School of Medicine, LSUHSC, New Orleans, LA, United States of America
| | | | - William C. Gordon
- Neuroscience Center, School of Medicine, LSUHSC, New Orleans, LA, United States of America
- Department of Ophthalmology, School of Medicine, LSUHSC, New Orleans, LA, United States of America
| | - Nicolas G. Bazan
- Neuroscience Center, School of Medicine, LSUHSC, New Orleans, LA, United States of America
| | - Hamilton E. Farris
- Neuroscience Center, School of Medicine, LSUHSC, New Orleans, LA, United States of America
- Department Cell Biology and Anatomy, School of Medicine, LSUHSC, New Orleans, LA, United States of America
- Department of Otolaryngology & Biocommunication, School of Medicine, LSUHSC, New Orleans, LA, United States of America
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2
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Dittrich C, Hoelzl F, Smith S, Fouilloux CA, Parker DJ, O’Connell LA, Knowles LS, Hughes M, Fewings A, Morgan R, Rojas B, Comeault AA. Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution. Genome Biol Evol 2024; 16:evae109. [PMID: 38753031 PMCID: PMC11152451 DOI: 10.1093/gbe/evae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2024] [Indexed: 06/07/2024] Open
Abstract
Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.
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Affiliation(s)
- Carolin Dittrich
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Franz Hoelzl
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Chloe A Fouilloux
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Darren J Parker
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | | | - Lucy S Knowles
- NERC Environmental Omics Facility, University of Sheffield, Sheffield, UK
| | - Margaret Hughes
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Ade Fewings
- Supercomputing Wales, Digital Services, Bangor University, Bangor, UK
| | - Rhys Morgan
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | - Bibiana Rojas
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Aaron A Comeault
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
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3
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Medeiros LADE, Gentil E, Kaefer IL, Cohn-Haft M. Distribution and diversification of Adelphobates, emblematic poison frogs from Brazilian Amazonia. AN ACAD BRAS CIENC 2024; 96:e20230659. [PMID: 38655924 DOI: 10.1590/0001-3765202320230659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/16/2023] [Indexed: 04/26/2024] Open
Abstract
Adelphobates contains three species, and the inaccurate identification of A. quinquevittatus and the scarcity of records of A. castaneoticus complicate inference of their distributions; the latter species occurs in sympatry with A. galactonotus. Our objective was to revise the distributions of Adelphobates by compiling data and modeling habitat suitability, as range limits may be shaped by landscape features and biotic interactions. We initially analyzed the existence of operational taxonomic units within the nominal species and subsequently inferred the observed and potential distributions, taking into account the possible independent lineages for the three species, and we also generated a molecular timetree to understand the chronology of interspecific diversification events. Adelphobates quinquevittatus was found to have a more easterly distribution than previously described, and specimens with phenotypic variation were found to occur in areas inconsistent with the modeling, and A. castaneoticus was concentrated in the Tapajós-Xingu interfluve, surrounded by A. galactonotus. Models indicated that the right bank of the Xingu River is suitable for both species, indeed, both were found there. Despite Adelphobates species having their distributions delimited by major Amazonian rivers, estimated divergence times predate the formation of the modern river network, suggesting that other mechanisms were involved in their diversification.
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Affiliation(s)
- Larissa A DE Medeiros
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
| | - Eduardo Gentil
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
| | - Igor L Kaefer
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Av. Rodrigo Otávio, 6200, Coroado I, 69077-000 Manaus, AM, Brazil
| | - Mario Cohn-Haft
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Aves, Coordenação de Pesquisas em Biodiversidade, Av. André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
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4
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Twomey E, Melo-Sampaio P, Schulte LM, Bossuyt F, Brown JL, Castroviejo-Fisher S. Multiple Routes to Color Convergence in a Radiation of Neotropical Poison Frogs. Syst Biol 2023; 72:1247-1261. [PMID: 37561391 PMCID: PMC10924724 DOI: 10.1093/sysbio/syad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023] Open
Abstract
Convergent evolution is defined as the independent evolution of similar phenotypes in different lineages. Its existence underscores the importance of external selection pressures in evolutionary history, revealing how functionally similar adaptations can evolve in response to persistent ecological challenges through a diversity of evolutionary routes. However, many examples of convergence, particularly among closely related species, involve parallel changes in the same genes or developmental pathways, raising the possibility that homology at deeper mechanistic levels is an important facilitator of phenotypic convergence. Using the genus Ranitomeya, a young, color-diverse radiation of Neotropical poison frogs, we set out to 1) provide a phylogenetic framework for this group, 2) leverage this framework to determine if color phenotypes are convergent, and 3) to characterize the underlying coloration mechanisms to test whether color convergence occurred through the same or different physical mechanisms. We generated a phylogeny for Ranitomeya using ultraconserved elements and investigated the physical mechanisms underlying bright coloration, focusing on skin pigments. Using phylogenetic comparative methods, we identified several instances of color convergence, involving several gains and losses of carotenoid and pterin pigments. We also found a compelling example of nonparallel convergence, where, in one lineage, red coloration evolved through the red pterin pigment drosopterin, and in another lineage through red ketocarotenoids. Additionally, in another lineage, "reddish" coloration evolved predominantly through structural color mechanisms. Our study demonstrates that, even within a radiation of closely related species, convergent evolution can occur through both parallel and nonparallel mechanisms, challenging the assumption that similar phenotypes among close relatives evolve through the same mechanisms.
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Affiliation(s)
- Evan Twomey
- Department of Wildlife/Zoo Animal Biology and Systematics, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
| | - Paulo Melo-Sampaio
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, R. Gen. Herculano Gomes 41, Rio de Janeiro 20941-360, Brazil
| | - Lisa M Schulte
- Department of Wildlife/Zoo Animal Biology and Systematics, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
| | - Franky Bossuyt
- Amphibian Evolution Laboratory, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Jason L Brown
- School of Biological Sciences, Southern Illinois University, 125 Lincoln Dr., Carbondale, IL 62901, USA
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5
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Gonzalez M, Carazzone C. Eco-Metabolomics Applied to the Chemical Ecology of Poison Frogs (Dendrobatoidea). J Chem Ecol 2023; 49:570-598. [PMID: 37594619 PMCID: PMC10725362 DOI: 10.1007/s10886-023-01443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023]
Abstract
Amphibians are one of the most remarkable sources of unique natural products. Biogenic amines, peptides, bufodienolides, alkaloids, and volatile organic compounds have been characterized in different species. The superfamily Dendrobatoidea represents one of the most enigmatic cases of study in chemical ecology because their skin secretome is composed by a complex mixture (i.e. cocktail) of highly lethal and noxious unique alkaloid structures. While chemical defences from dendrobatoids (families Dendrobatidae and Aromobatidae) have been investigated employing ecological, behavioral, phylogenetic and evolutionary perspectives, studies about the analytical techniques needed to perform the chemical characterization have been neglected for many years. Therefore, our aim is to summarize the current methods applied for the characterization of chemical profiles in dendrobatoids and to illustrate innovative Eco-metabolomics strategies that could be translated to this study model. This approach could be extended to natural products other than alkaloids and implemented for the chemical analysis of different species of dendrobatoids employing both low- and high-resolution mass spectrometers. Here, we overview important biological features to be considered, procedures that could be applied to perform the chemical characterization, steps and tools to perform an Eco-metabolomic analysis, and a final discussion about future perspectives.
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Affiliation(s)
- Mabel Gonzalez
- Department of Chemistry, Universidad de los Andes, 4976, Bogotá, AA, Colombia.
- Department of Biology, Stanford University, Palo Alto, CA, 94305, USA.
| | - Chiara Carazzone
- Department of Chemistry, Universidad de los Andes, 4976, Bogotá, AA, Colombia.
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6
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Zhang J, Li Z, Lai J, Zhang Z, Zhang F. A novel probe set for the phylogenomics and evolution of RTA spiders. Cladistics 2023; 39:116-128. [PMID: 36719825 DOI: 10.1111/cla.12523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 02/01/2023] Open
Abstract
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.
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Affiliation(s)
- Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zhaoyi Li
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Jiaxing Lai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zhisheng Zhang
- School of Life Sciences, Southwest University, Chongqing, 400700, China
| | - Feng Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
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7
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Medina-Ortiz K, Navia F, Mosquera-Gil C, Sánchez A, Sterling G, Fierro L, Castaño S. Identification of the NA +/K +-ATPase α-Isoforms in Six Species of Poison Dart Frogs and their Sensitivity to Cardiotonic Steroids. J Chem Ecol 2023; 49:116-132. [PMID: 36877397 PMCID: PMC10102066 DOI: 10.1007/s10886-023-01404-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 03/07/2023]
Abstract
Cardiotonic steroids (CTS) are a group of compounds known to be toxic due to their ability to inhibit the Na+/K+-ATPase (NKA), which is essential to maintain the balance of ions in animal cells. An evolutionary strategy of molecular adaptation to avoid self-intoxication acquired by CTS defended organisms and their predators is the structural modification of their NKA where specific amino acid substitutions confer resistant phenotypes. Several lineages of poison dart frogs (Dendrobatidae) are well known to sequester a wide variety of lipophilic alkaloids from their arthropod diet, however there is no evidence of CTS-sequestration or dietary exposure. Interestingly this study identified the presence of α-NKA isoforms (α1 and α2) with amino acid substitutions indicative of CTS-resistant phenotypes in skeletal muscle transcriptomes obtained from six species of dendrobatids: Phyllobates aurotaenia, Oophaga anchicayensis, Epipedobates boulengeri, Andinobates bombetes, Andinobates minutus, and Leucostethus brachistriatus, collected in the Valle del Cauca (Colombia). P. aurotaenia, A. minutus, and E. boulengeri presented two variants for α1-NKA, with one of them having these substitutions. In contrast, O. anchicayensis and A. bombetes have only one α1-NKA isoform with an amino acid sequence indicative of CTS susceptibility and an α2-NKA with one substitution that could confer a reduced affinity for CTS. The α1 and α2 isoforms of L. brachistriatus do not contain substitutions imparting CTS resistance. Our findings indicate that poison dart frogs express α-NKA isoforms with different affinities for CTS and the pattern of this expression might be influenced by factors related to evolutionary, physiological, ecological, and geographical burdens.
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Affiliation(s)
- Katherine Medina-Ortiz
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia.
| | - Felipe Navia
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Claudia Mosquera-Gil
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Adalberto Sánchez
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Gonzalo Sterling
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Leonardo Fierro
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Santiago Castaño
- Laboratorio de Herpetología Y Toxinología, Department of Physiological Sciences, Faculty of Health, Universidad del Valle, Cali, Colombia.
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8
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Barnett JB, Yeager J, McEwen BL, Kinley I, Anderson HM, Guevara J. Size-dependent colouration balances conspicuous aposematism and camouflage. J Evol Biol 2022. [PMID: 36514842 DOI: 10.1111/jeb.14143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/09/2022] [Indexed: 12/15/2022]
Abstract
Colour is an important component of many different defensive strategies, but signal efficacy and detectability will also depend on the size of the coloured structures, and how pattern size interacts with the background. Consequently, size-dependent changes in colouration are common among many different species as juveniles and adults frequently use colour for different purposes in different environmental contexts. A widespread strategy in many species is switching from crypsis to conspicuous aposematic signalling as increasing body size can reduce the efficacy of camouflage, while other antipredator defences may strengthen. Curiously, despite being chemically defended, the gold-striped frog (Lithodytes lineatus, Leptodactylidae) appears to do the opposite, with bright yellow stripes found in smaller individuals, whereas larger frogs exhibit dull brown stripes. Here, we investigated whether size-dependent differences in colour support distinct defensive strategies. We first used visual modelling of potential predators to assess how colour contrast varied among frogs of different sizes. We found that contrast peaked in mid-sized individuals while the largest individuals had the least contrasting patterns. We then used two detection experiments with human participants to evaluate how colour and body size affected overall detectability. These experiments revealed that larger body sizes were easier to detect, but that the colours of smaller frogs were more detectable than those of larger frogs. Taken together our data support the hypothesis that the primary defensive strategy changes from conspicuous aposematism to camouflage with increasing size, implying size-dependent differences in the efficacy of defensive colouration. We discuss our data in relation to theories of size-dependent aposematism and evaluate the evidence for and against a possible size-dependent mimicry complex with sympatric poison frogs (Dendrobatidae).
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Affiliation(s)
- James B Barnett
- Department of Psychology, Neuroscience & Behaviour, McMaster University, Ontario, Hamilton, Canada
| | - Justin Yeager
- Biodiversidad Medio Ambiente y Salud (BIOMAS), Direccion General de Investigacion, Universidad de las Américas, Quito, Ecuador
| | - Brendan L McEwen
- Department of Psychology, Neuroscience & Behaviour, McMaster University, Ontario, Hamilton, Canada
| | - Isaac Kinley
- Department of Psychology, Neuroscience & Behaviour, McMaster University, Ontario, Hamilton, Canada
| | - Hannah M Anderson
- Department of Psychology, Neuroscience & Behaviour, McMaster University, Ontario, Hamilton, Canada
| | - Jennifer Guevara
- Department of Psychology, Neuroscience & Behaviour, McMaster University, Ontario, Hamilton, Canada.,Grupo de Investigación Ecosistemas Tropicales y Cambio Global, Facultad Ciencias de la Vida, Universidad Regional Amazónica Ikiam, Tena, Ecuador
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9
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Muell MR, Chávez G, Prates I, Guillory WX, Kahn TR, Twomey EM, Rodrigues MT, Brown JL. Phylogenomic analysis of evolutionary relationships in Ranitomeya poison frogs (Family Dendrobatidae) using ultraconserved elements. Mol Phylogenet Evol 2022; 168:107389. [PMID: 35026428 DOI: 10.1016/j.ympev.2022.107389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
The use of genome-scale data in phylogenetics has enabled recent strides in determining the relationships between taxa that are taxonomically problematic because of extensive morphological variation. Here, we employ a phylogenomic approach to infer evolutionary relationships within Ranitomeya (Anura: Dendrobatidae), an Amazonian lineage of poison frogs consisting of 16 species with remarkable diversity in color pattern, range size, and parental care behavior. We infer phylogenies with all described species of Ranitomeya from ultraconserved nuclear genomic elements (UCEs) and also estimate divergence times. Our results differ from previous analyses regarding interspecific relationships. Notably, we find that R. toraro and R. defleri are not sister species but rather distantly related, contrary to previous analyses based on smaller genetic datasets. We recover R. uakarii as paraphyletic, designate certain populations formerly assigned to R. fantastica from Peru as R. summersi, and transfer the French Guianan and eastern Brazilian R. amazonica populations to R. variabilis. By clarifying both inter- and intraspecific relationships within Ranitomeya, our study paves the way for future tests of hypotheses on color pattern evolution and historical biogeography.
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Affiliation(s)
- Morgan R Muell
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| | - Germán Chávez
- Instituto Peruano de Herpetología, Lima, Perú; División de Herpetología - CORBIDI, Lima, Perú
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wilson X Guillory
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA; Department of Biological Sciences, Rutgers University Newark, Newark, NJ, USA
| | - Ted R Kahn
- Species Survival Commission (SSC), International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Evan M Twomey
- Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Jason L Brown
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
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10
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Ortega-Andrade HM, Rodes Blanco M, Cisneros-Heredia DF, Guerra Arévalo N, López de Vargas-Machuca KG, Sánchez-Nivicela JC, Armijos-Ojeda D, Cáceres Andrade JF, Reyes-Puig C, Quezada Riera AB, Székely P, Rojas Soto OR, Székely D, Guayasamin JM, Siavichay Pesántez FR, Amador L, Betancourt R, Ramírez-Jaramillo SM, Timbe-Borja B, Gómez Laporta M, Webster Bernal JF, Oyagata Cachimuel LA, Chávez Jácome D, Posse V, Valle-Piñuela C, Padilla Jiménez D, Reyes-Puig JP, Terán-Valdez A, Coloma LA, Pérez Lara MB, Carvajal-Endara S, Urgilés M, Yánez Muñoz MH. Red List assessment of amphibian species of Ecuador: A multidimensional approach for their conservation. PLoS One 2021; 16:e0251027. [PMID: 33956885 PMCID: PMC8101765 DOI: 10.1371/journal.pone.0251027] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/19/2021] [Indexed: 12/26/2022] Open
Abstract
Ecuador is one of the most biodiverse countries in the world, but faces severe pressures and threats to its natural ecosystems. Numerous species have declined and require to be objectively evaluated and quantified, as a step towards the development of conservation strategies. Herein, we present an updated National Red List Assessment for amphibian species of Ecuador, with one of the most detailed and complete coverages for any Ecuadorian taxonomic group to date. Based on standardized methodologies that integrate taxonomic work, spatial analyses, and ecological niche modeling, we assessed the extinction risk and identified the main threats for all Ecuadorian native amphibians (635 species), using the IUCN Red List Categories and Criteria. Our evaluation reveals that 57% (363 species) are categorized as Threatened, 12% (78 species) as Near Threatened, 4% (26 species) as Data Deficient, and 27% (168 species) as Least Concern. Our assessment almost doubles the number of threatened species in comparison with previous evaluations. In addition to habitat loss, the expansion of the agricultural/cattle raising frontier and other anthropogenic threats (roads, human settlements, and mining/oil activities) amplify the incidence of other pressures as relevant predictors of ecological integrity. Potential synergic effects with climate change and emergent diseases (apparently responsible for the sudden declines), had particular importance amongst the threats sustained by Ecuadorian amphibians. Most threatened species are distributed in montane forests and paramo habitats of the Andes, with nearly 10% of them occurring outside the National System of Protected Areas of the Ecuadorian government. Based on our results, we recommend the following actions: (i) An increase of the National System of Protected Areas to include threatened species. (ii) Supporting the ex/in-situ conservation programs to protect species considered like Critically Endangered and Endangered. (iii) Focalizing research efforts towards the description of new species, as well as species currently categorized as Data Deficient (DD) that may turn out to be threatened. The implementation of the described actions is challenging, but urgent, given the current conservation crisis faced by amphibians.
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Affiliation(s)
- H. Mauricio Ortega-Andrade
- Grupo de Biogeografía y Ecología Espacial, Universidad Regional Amazónica Ikiam, Tena, Ecuador
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- * E-mail:
| | - Marina Rodes Blanco
- Grupo de Biogeografía y Ecología Espacial, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | - Diego F. Cisneros-Heredia
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Instituto de Diversidad Biológica Tropical iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Nereida Guerra Arévalo
- Grupo de Biogeografía y Ecología Espacial, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | | | - Juan C. Sánchez-Nivicela
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Instituto de Diversidad Biológica Tropical iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Grupo de Investigación Evolución y Ecología de Fauna Neotropical, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Diego Armijos-Ojeda
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Carolina Reyes-Puig
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Instituto de Diversidad Biológica Tropical iBIOTROP, Museo de Zoología & Laboratorio de Zoología Terrestre, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | | | - Paul Székely
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Diana Székely
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto Biósfera USFQ, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Luis Amador
- Instituto de Ciencias Ambientales y Evolutivas, Doctorado en Ciencias m. Ecología y Evolución, Universidad Austral de Chile, Valdivia, Chile
| | | | | | | | | | | | | | - Daniel Chávez Jácome
- Instituto de Ciencias Ambientales y Evolutivas, Doctorado en Ciencias m. Ecología y Evolución, Universidad Austral de Chile, Valdivia, Chile
| | - Valentina Posse
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | | | - Juan Pablo Reyes-Puig
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
- Fundación Ecominga/Fundación Oscar Efrén Reyes, Baños, Ecuador
| | - Andrea Terán-Valdez
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | - Luis A. Coloma
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | | | - Sofía Carvajal-Endara
- Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Jambatu, Quito, Ecuador
| | - Miguel Urgilés
- Instituto Nacional de Biodiversidad, Casilla, Quito, Ecuador
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11
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Fischer MT, Ringler M, Ringler E, Pašukonis A. Reproductive behavior drives female space use in a sedentary Neotropical frog. PeerJ 2020; 8:e8920. [PMID: 32337103 PMCID: PMC7169969 DOI: 10.7717/peerj.8920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/16/2020] [Indexed: 12/04/2022] Open
Abstract
Longer-range movements of anuran amphibians such as mass migrations and habitat invasion have received a lot of attention, but fine-scale spatial behavior remains largely understudied. This gap is especially striking for species that show long-term site fidelity and display their whole behavioral repertoire in a small area. Studying fine-scale movement with conventional capture-mark-recapture techniques is difficult in inconspicuous amphibians: individuals are hard to find, repeated captures might affect their behavior and the number of data points is too low to allow a detailed interpretation of individual space use and time budgeting. In this study, we overcame these limitations by equipping females of the Brilliant-Thighed Poison Frog (Allobates femoralis) with a tag allowing frequent monitoring of their location and behavior. Neotropical poison frogs are well known for their complex behavior and diverse reproductive and parental care strategies. Although the ecology and behavior of the polygamous leaf-litter frog Allobates femoralis is well studied, little is known about the fine-scale space use of the non-territorial females who do not engage in acoustic and visual displays. We tracked 17 females for 6 to 17 days using a harmonic direction finder to provide the first precise analysis of female space use in this species. Females moved on average 1 m per hour and the fastest movement, over 20 m per hour, was related to a subsequent mating event. Traveled distances and activity patterns on days of courtship and mating differed considerably from days without reproduction. Frogs moved more on days with lower temperature and more precipitation, but mating seemed to be the main trigger for female movement. We observed 21 courtships of 12 tagged females. For seven females, we observed two consecutive mating events. Estimated home ranges after 14 days varied considerably between individuals and courtship and mating associated space use made up for ∼30% of the home range. Allobates femoralis females spent large parts of their time in one to three small centers of use. Females did not adjust their time or space use to the density of males in their surroundings and did not show wide-ranging exploratory behavior. Our study demonstrates how tracking combined with detailed behavioral observations can reveal the patterns and drivers of fine-scale spatial behavior in sedentary species.
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Affiliation(s)
| | - Max Ringler
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria.,Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Eva Ringler
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria.,Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria.,Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Vienna, Austria
| | - Andrius Pašukonis
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria.,Department of Biology, Stanford University, Stanford, CA, United States of America
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12
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Ebersbach J, Posso-Terranova A, Bogdanowicz S, Gómez-Díaz M, García-González MX, Bolívar-García W, Andrés J. Complex patterns of differentiation and gene flow underly the divergence of aposematic phenotypes in Oophaga poison frogs. Mol Ecol 2020; 29:1944-1956. [PMID: 31971303 DOI: 10.1111/mec.15360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/11/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022]
Abstract
Hybridization and introgression can have complex consequences for both species evolution and conservation. Here, we investigated the origin and characteristics of a putative hybrid zone between two South American poison dart frog species, Oophaga anchicayensis and the critically endangered Oophaga lehmanni, which are heavily sought after on the illegal pet market. Using a combination of phenotypic (49 traits) and genomic (ddRADseq) data, we found that the putative hybrids are morphologically distinct from their parental species and confirmed genomic signatures of admixture in these populations. Several lines of evidence (hybrid indices, interspecific hybrid heterozygosity, genomic clines, comparisons with simulated hybrids and demographic modelling) support the conclusion that these populations are not comprised of early-generation hybrids and thus, they probably did not arise as a result of illegal translocations associated with wildlife trafficking. Instead, they probably represent an independent lineage which has persisted through isolation and has only relatively recently re-established gene flow with both parental species. Furthermore, we detected signals of differential introgression from parental species into these hybrid populations which suggest relaxed stabilizing selection on these aposematic colour morphs, potentially via context-dependent female choice. These populations thus provide a fascinating window into the role of hybridization, isolation and female choice in the diversification of South American poison dart frogs. In addition, our results underline the importance of landscape conservation measures to protect, not only known localities of nominal species, but also the phenotypic and genomic variation harbored by admixed lineages which represent crucial repositories for the impressive diversity in this system.
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Affiliation(s)
- Jana Ebersbach
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Andrés Posso-Terranova
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia sede Palmira, Palmira, Colombia
| | - Steven Bogdanowicz
- Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
| | - Mónica Gómez-Díaz
- Research Group in Animal Ecology, Department of Biology, Universidad del Valle, Cali, Colombia
| | | | - Wilmar Bolívar-García
- Research Group in Animal Ecology, Department of Biology, Universidad del Valle, Cali, Colombia
| | - José Andrés
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
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13
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Stückler S, Ringler M, Pašukonis A, Weinlein S, Hödl W, Ringler E. Spatio-Temporal Characteristics of the Prolonged Courtship in Brilliant-Thighed Poison Frogs, Allobates femoralis. HERPETOLOGICA 2019. [DOI: 10.1655/herpetologica-d-19-00010.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Susanne Stückler
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Max Ringler
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Andrius Pašukonis
- Department of Cognitive Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Steffen Weinlein
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Walter Hödl
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Eva Ringler
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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14
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Santos VM, Silva Cáceres ME, Lücking R. Diversity of foliicolous lichens in isolated montane rainforests (Brejos) of northeastern Brazil and their biogeography in a neotropical context. Ecol Res 2019. [DOI: 10.1111/1440-1703.12071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viviane M. Santos
- Centro de Biociências, Departamento de Micologia Universidade Federal de Pernambuco Recife Brazil
- Departamento de Biociências Universidade Federal de Sergipe Itabaiana Brazil
| | - Marcela E. Silva Cáceres
- Centro de Biociências, Departamento de Micologia Universidade Federal de Pernambuco Recife Brazil
- Departamento de Biociências Universidade Federal de Sergipe Itabaiana Brazil
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum Freie Universität Berlin Berlin Germany
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15
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Guillory WX, French CM, Twomey EM, Chávez G, Prates I, von May R, De la Riva I, Lötters S, Reichle S, Serrano-Rojas SJ, Whitworth A, Brown JL. Phylogenetic relationships and systematics of the Amazonian poison frog genus Ameerega using ultraconserved genomic elements. Mol Phylogenet Evol 2019; 142:106638. [PMID: 31586688 DOI: 10.1016/j.ympev.2019.106638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/02/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022]
Abstract
The Amazonian poison frog genus Ameerega is one of the largest yet most understudied of the brightly colored genera in the anuran family Dendrobatidae, with 30 described species ranging throughout tropical South America. Phylogenetic analyses of Ameerega are highly discordant, lacking consistency due to variation in data types and methods, and often with limited coverage of species diversity in the genus. Here, we present a comprehensive phylogenomic reconstruction of Ameerega, utilizing state-of-the-art sequence capture techniques and phylogenetic methods. We sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. We generated topologies using maximum likelihood and coalescent methods and compared the use of maximum likelihood and Bayesian methods for estimating divergence times. Our phylogenetic inference diverged strongly from those of previous studies, and we recommend steps to bring Ameerega taxonomy in line with the new phylogeny. We place several species in a phylogeny for the first time, as well as provide evidence for six potential candidate species. We estimate that Ameerega experienced a rapid radiation approximately 7-11 million years ago and that the ancestor of all Ameerega was likely an aposematic, montane species. This study underscores the utility of phylogenomic data in improving our understanding of the phylogeny of understudied clades and making novel inferences about their evolution.
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Affiliation(s)
- Wilson X Guillory
- Department of Zoology, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL 62901, USA.
| | - Connor M French
- Department of Zoology, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL 62901, USA; Department of Biology, Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Evan M Twomey
- Pontificia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Germán Chávez
- División de Herpetología, Centro de Ornitología y Biodiversidad (CORBIDI), Santa Rita N°105 36 Of. 202, Urb. Huertos de San Antonio, Santiago de Surco, Lima, Peru
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave, NW, Washington, DC 20560-0162, USA
| | - Rudolf von May
- Biology Program, California State University Channel Islands, 1 University Drive, Camarillo, CA 93012, USA
| | - Ignacio De la Riva
- Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Stefan Lötters
- Department of Biogeography, Universität Trier, Universitätsring 15, 54296, Trier, Germany
| | | | - Shirley J Serrano-Rojas
- Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew Whitworth
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jason L Brown
- Department of Zoology, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL 62901, USA
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